| 37 |
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* arising out of the use of or inability to use software, even if the |
| 38 |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
| 40 |
+ |
* |
| 41 |
+ |
* BondOrderParameter.cpp |
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+ |
* OOPSE-4 |
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+ |
* |
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+ |
* Created by J. Daniel Gezelter on 09/26/06. |
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+ |
* @author J. Daniel Gezelter |
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+ |
* @version $Id: BondOrderParameter.cpp,v 1.20 2006-11-03 22:02:55 gezelter Exp $ |
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+ |
* |
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*/ |
| 41 |
– |
|
| 42 |
– |
|
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/* Creates orientational bond order parameters as outlined by |
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* Bond-orientaional order in liquids and glasses, Steinhart,Nelson,Ronchetti |
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* Phys Rev B, 28,784,1983 |
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* |
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– |
*/ |
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|
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#include "applications/staticProps/BondOrderParameter.hpp" |
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#include "utils/simError.h" |
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} |
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} |
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} |
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+ |
delete [] THRCOF; |
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+ |
THRCOF = NULL; |
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} |
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|
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BondOrderParameter::~BondOrderParameter() { |
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Q_histogram_.clear(); |
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W_histogram_.clear(); |
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+ |
for (int l = 0; l <= lMax_; l++) { |
| 130 |
+ |
for (int m = -l; m <= l; m++) { |
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+ |
w3j[std::make_pair(l,m)].clear(); |
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+ |
} |
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+ |
} |
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+ |
w3j.clear(); |
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+ |
m2Min.clear(); |
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+ |
m2Max.clear(); |
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} |
| 138 |
< |
|
| 138 |
> |
|
| 139 |
|
void BondOrderParameter::initalizeHistogram() { |
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for (int bin = 0; bin < nBins_; bin++) { |
| 141 |
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for (int l = 0; l <= lMax_; l++) { |
| 230 |
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if (atom->getGlobalIndex() != myIndex) { |
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|
|
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|
vec = sd->getPos() - atom->getPos(); |
| 233 |
< |
currentSnapshot_->wrapVector(vec); |
| 233 |
> |
|
| 234 |
> |
if (usePeriodicBoundaryConditions_) |
| 235 |
> |
currentSnapshot_->wrapVector(vec); |
| 236 |
|
|
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// Calculate "bonds" and build Q_lm(r) where |
| 238 |
|
// Q_lm = Y_lm(theta(r),phi(r)) |
| 398 |
|
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
| 399 |
|
osq << Qval; |
| 400 |
|
for (int l = 0; l <= lMax_; l++) { |
| 401 |
< |
osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l]; |
| 401 |
> |
osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]*deltaQ_/ |
| 402 |
> |
(RealType)Qcount_[l]; |
| 403 |
|
} |
| 404 |
|
osq << "\n"; |
| 405 |
|
} |
| 420 |
|
osw << "# selection: (" << selectionScript_ << ")\n"; |
| 421 |
|
osw << "# \n"; |
| 422 |
|
for (int l = 0; l <= lMax_; l++) { |
| 423 |
< |
osw << "# <W_" << l << ">: " << real(What[l]) << "\n"; |
| 423 |
> |
osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n"; |
| 424 |
|
} |
| 425 |
|
// Normalize by number of frames and write it out: |
| 426 |
|
for (int i = 0; i < nBins_; ++i) { |
| 427 |
|
RealType Wval = MinW_ + (i + 0.5) * deltaW_; |
| 428 |
|
osw << Wval; |
| 429 |
|
for (int l = 0; l <= lMax_; l++) { |
| 430 |
< |
osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] / (RealType)Wcount_[l]; |
| 430 |
> |
osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]*deltaW_/ |
| 431 |
> |
(RealType)Wcount_[l]; |
| 432 |
|
} |
| 433 |
|
osw << "\n"; |
| 434 |
|
} |
